The collapse of the New Order lifted the lid on simmering communal tensions in many regions of Indonesia. During the New Order violent conflicts between local ethnic and religious communities had broken out from time to time, but from 1998 to the early 2000s the extent and intensity of violence increased sharply. Rioting in cities and towns caused many casualties and damage to property but usually lasted no more than a few days. In several regions, however, conflicts took the form of one-sided massacres while in others they were more akin to civil war. By the early 2000s, the number of lives lost in these conflicts had exceeded ten thousand and well over a million refugees had been forced to flee their homes to which many never returned. In East Timor, Aceh and Papua, the weakening of central authority provided the opportunity for the resurgence of existing separatist movements, one of which is discussed in the case study of the Aceh conflict in Chapter 8. In West and Central Kalimantan, Poso and Maluku, communal conflict intensified to a level that was beyond the capacity of the state to contain, as will be illustrated by the case of Maluku in this chapter. These regions — whether afflicted by separatist or communal conflict — were overwhelmed by crises in which the state ceased to function effectively. If they had been independent countries, they would have been classified as “failed states” but in fact, of course, they — except East Timor — remained part of the Republic of Indonesia. As we will see in the cases of both Aceh and Maluku, these regional conflicts had local origins but were also linked to political rivalries at the national level.

Maluku had been perceived as a peaceful region in which relations between Muslims and Christians were relatively harmonious. A complex combination of disparate factors, however, contributed to the breakdown of order in Maluku after the fall of the New Order regime. Demographic change had upset the balance between the two religious communities, the holding of free elections exacerbated uncertainty about the new constellation of power, national politics under Soeharto had encouraged increased Muslim assertiveness, divided religious loyalties immobilized local security forces, and radical Muslim groups outside Maluku sent militia forces to fight alongside their co-religionists.